The problem is the mask is z-index:0 or 1 and passing a z-index to the dialog doesn't change the mask z-index. I set them both to a ridiculous z-index in one shot in the css file and never worry about it again.

I actually found it on my own (Aptana wasn't showing it in the outline for whatever reason) but anyway, it does not change anything...
I'll try to change these absolute positioned elements tommorow, and i'll see if that's not the cause. I don't know I have the feeling only the parts not covered by one of these elements are affected by the mask, but for now, time to sleep